ArticleHuman heredity2009
Linkage analysis with dense SNP maps in isolated populations.
Article in Human heredity, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 18 citations in OpenAlex.
- Determinants of Human Asymmetry: Does Asymmetrical Retinal Vasculature Predict Asymmetry Elsewhere in the Body?Life (Basel, Switzerland) · 2024Article
- Can whole-exome sequencing data be used for linkage analysis?European journal of human genetics : EJHG · 2016Article
- PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers.Bioinformatics (Oxford, England) · 2015Article
- A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees.Bioinformatics (Oxford, England) · 2013Article
- Small effective population size and genetic homogeneity in the Val Borbera isolate.European journal of human genetics : EJHG · 2013Article
- The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes.Human molecular genetics · 2012Article
- Obtaining accurate p values from a dense SNP linkage scan.Human heredity · 2012Article
- Finding disease genes: a fast and flexible approach for analyzing high-throughput data.European journal of human genetics : EJHG · 2011Article
- Identity by descent estimation with dense genome-wide genotype data.Genetic epidemiology · 2011Article
- Does inbreeding affect N-glycosylation of human plasma proteins?Molecular genetics and genomics : MGG · 2011Article
- Consanguinity around the world: what do the genomic data of the HGDP-CEPH diversity panel tell us?European journal of human genetics : EJHG · 2011Article
- Genome wide linkage study, using a 250K SNP map, of Plasmodium falciparum infection and mild malaria attack in a Senegalese population.PloS one · 2010Article
- Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data.BMC genomics · 2010Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
Abstract
objectiveSNP maps are becoming the gold standard for genetic markers, even for linkage analyses. However, because of the density of SNPs on most high throughput platforms, the resulting significant linkage disequilibrium (LD) can bias classical nonparametric multipoint linkage analyses. This problem may be even stronger in population isolates where LD can extend over larger distances and with a more stochastic pattern. We investigate the issue of linkage analysis with SNPs from the Affymetrix 500K GeneChip array in extended families from the isolated Hutterite population.
methodsWe minimized LD between SNPs by two methods based on a LD block pattern (Merlin and SNPLINK) and by MASEL, a new algorithm that we proposed to select SNP subsets with minimum LD and with no prior hypothesis about the LD pattern.
resultsSimulations, performed using the real LD pattern observed in the Hutterite population, show that sizeable inflation of linkage statistics persist when LD between SNPs is minimized by Merlin and SNPLINK. Inflation of linkage statistics is better controlled with MASEL.
conclusionIn this population, it may be difficult to extract from standard GeneChip arrays a SNP map without LD-driven bias that is more informative than a dense microsatellite map.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.